Contacts of the helix formed by residues 327 - 343 (chain C) in PDB entry 3IAD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 327 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C TYR* 3.5 14.3 - - - -
320C HIS 3.5 17.5 - - - +
321C ALA* 5.3 1.3 + - - -
323C VAL 2.7 28.3 + - - +
324C ALA 2.8 24.2 + - - -
325C TYR 2.6 14.2 + - - +
326C HIS* 1.3 73.8 - - - +
328C ASN* 1.3 71.2 + - - +
329C ILE* 2.9 40.2 + - - +
330C HIS* 3.0 12.1 + - - +
331C ALA 3.1 9.7 + - - -
498C TRP* 5.2 0.9 - - - -
501C ARG* 3.8 9.9 - - - +
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Residues in contact with ASN 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ASN* 3.3 37.2 + - - +
283C PRO* 3.3 12.1 - - - +
284C LEU* 4.0 6.8 - - + +
316C GLU* 3.0 42.1 + - + +
319C TYR* 3.5 24.4 - - + +
320C HIS 5.3 0.9 - - - +
321C ALA* 5.4 5.0 - - - -
327C ASN* 1.3 81.1 - - - +
329C ILE* 1.3 61.4 + - - +
331C ALA* 3.6 5.0 - - - +
332C ALA* 3.0 28.4 + - - +
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Residues in contact with ILE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 4.0 23.2 - - + +
273C PHE* 3.8 32.1 - - + -
276C ALA* 4.0 13.2 - - + -
281C ASN* 4.6 6.5 - - - +
283C PRO* 4.1 19.1 - - + -
327C ASN* 2.9 16.4 + - - +
328C ASN* 1.3 83.6 - - - +
330C HIS* 1.3 58.2 + - - +
332C ALA* 3.5 2.4 + - - +
333C ASP* 2.9 27.0 + - - +
498C TRP* 3.8 17.5 - - + -
501C ARG* 4.0 18.4 - - - +
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Residues in contact with HIS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 3.2 61.3 + + - +
326C HIS* 4.5 3.8 - + - -
327C ASN* 3.0 8.7 + - - +
329C ILE* 1.3 76.3 - - - +
331C ALA* 1.3 66.2 + - - +
333C ASP* 3.3 7.0 + - - +
334C VAL* 2.9 37.0 + - + +
366C HIS* 3.3 8.3 + + - -
367C ASP* 3.3 12.3 - - + -
483C ALA 5.5 0.2 - - - -
484C ASP* 3.0 19.2 + - - -
487C ASN* 5.2 1.1 + - - -
498C TRP* 3.7 16.7 - - + -
620C ZN 2.2 32.7 - - - -
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 4.0 11.9 - - + -
319C TYR* 3.4 43.3 - - + +
327C ASN 3.1 6.2 + - - +
328C ASN 3.6 8.1 - - - +
329C ILE 3.3 0.2 - - - -
330C HIS* 1.3 83.2 - - - +
332C ALA* 1.3 62.8 + - - +
334C VAL* 3.4 2.1 + - - +
335C VAL* 2.9 30.2 + - - +
363C SER 3.9 6.1 - - - +
364C ALA 4.0 4.3 - - - +
366C HIS* 4.6 2.7 - - - -
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Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 4.4 1.3 - - + -
283C PRO* 3.8 6.7 - - + -
284C LEU* 3.8 28.4 - - - +
287C ILE* 3.8 28.8 - - + +
328C ASN 3.0 17.6 + - - +
329C ILE 3.6 4.9 - - - +
330C HIS 3.3 0.2 - - - -
331C ALA* 1.3 75.8 - - - +
333C ASP* 1.3 59.3 + - - +
335C VAL* 3.0 5.7 + - - +
336C GLN* 2.8 31.9 + - - +
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Residues in contact with ASP 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 4.2 17.9 - - + +
329C ILE 2.9 18.7 + - - +
330C HIS* 3.6 9.4 + - - +
332C ALA* 1.3 76.2 - - - +
334C VAL* 1.3 59.2 + - - +
336C GLN* 3.3 7.1 + - - +
337C SER* 2.9 34.0 + - - -
483C ALA 5.2 0.2 - - - +
486C SER* 4.3 4.5 + - - -
487C ASN* 3.6 18.2 + - - -
490C LYS* 2.9 29.9 + - - -
498C TRP* 3.5 31.1 + - + -
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Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C HIS* 2.9 52.3 + - + +
331C ALA 3.8 1.8 - - - +
333C ASP* 1.3 76.5 - - - +
335C VAL* 1.3 57.2 + - - +
337C SER* 3.9 5.2 - - - -
338C THR* 3.0 29.5 + - - -
363C SER* 4.0 13.2 - - - +
366C HIS* 3.5 25.6 - - + +
480C VAL* 4.3 11.4 - - + +
483C ALA* 3.9 26.4 - - + +
484C ASP* 3.9 5.8 - - + +
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 4.0 7.9 - - + -
287C ILE* 4.8 2.7 - - + -
288C MET* 3.8 23.6 - - + -
291C ILE* 3.7 20.0 - - + -
331C ALA 2.9 18.8 + - - +
332C ALA* 3.0 9.6 + - - +
334C VAL* 1.3 75.2 - - - +
336C GLN* 1.3 57.7 + - - +
338C THR* 3.2 5.0 + - - +
339C HIS* 3.0 26.0 + - - +
360C ILE* 4.0 12.6 - - + +
363C SER* 3.7 9.0 - - - -
364C ALA* 3.5 39.9 - - + +
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Residues in contact with GLN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C VAL* 3.0 33.1 + - + +
267C LYS 2.8 29.3 + - - +
268C TRP* 4.6 1.3 - - - +
269C GLY 5.1 0.3 + - - -
270C LEU* 3.6 33.6 + - + +
287C ILE* 4.0 12.1 - - + -
291C ILE* 4.0 9.4 - - - -
332C ALA 2.8 19.0 + - - +
333C ASP* 3.9 5.8 - - - +
335C VAL* 1.3 74.7 - - - +
337C SER* 1.3 66.5 + - - +
339C HIS* 3.4 2.3 + - - +
340C VAL* 3.1 37.1 + - - +
490C LYS* 4.1 9.7 + - - -
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C TRP* 3.5 21.9 - - - -
333C ASP* 2.9 21.9 + - - -
334C VAL* 3.9 4.7 - - - -
335C VAL 3.2 0.2 - - - -
336C GLN* 1.3 75.9 - - - +
338C THR* 1.3 60.7 + - - +
340C VAL 3.4 0.7 + - - -
341C LEU* 3.1 34.1 + - - +
483C ALA* 3.9 17.7 - - - -
486C SER* 3.8 4.2 + - - -
490C LYS* 2.6 31.2 + - - -
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Residues in contact with THR 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C VAL 3.0 18.1 + - - -
335C VAL 3.7 3.1 - - - -
337C SER* 1.3 75.0 - - - +
339C HIS* 1.3 58.7 + - - +
341C LEU* 3.9 7.1 - - - +
342C LEU* 3.1 35.0 + - + +
359C ALA* 4.1 28.3 - - + +
360C ILE* 4.4 5.6 - - + -
363C SER* 3.2 24.2 + - - +
479C MET* 4.1 6.8 + - - +
480C VAL* 3.5 14.7 + - + +
483C ALA* 3.5 16.2 - - - +
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Residues in contact with HIS 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C VAL* 3.3 24.5 - - - +
266C ASN* 2.7 30.2 + - - -
291C ILE* 3.7 34.3 - - + +
294C GLU* 4.1 17.5 - - + +
295C ARG* 2.8 69.7 + - + +
335C VAL 3.0 13.3 + - - +
336C GLN 3.4 7.9 - - - +
337C SER 3.2 0.2 - - - -
338C THR* 1.3 76.5 - - - +
340C VAL* 1.3 64.7 + - + +
342C LEU* 4.7 2.2 - - - -
343C SER* 3.2 11.1 + - - -
360C ILE* 4.9 4.9 - - + +
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Residues in contact with VAL 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C VAL 4.0 2.2 - - - +
266C ASN* 3.6 27.6 - - - +
267C LYS 4.0 4.3 - - - -
268C TRP* 3.9 29.4 - - + +
336C GLN* 3.1 39.0 + - - +
337C SER 3.9 4.9 - - - +
338C THR 3.4 0.2 - - - -
339C HIS* 1.3 74.7 - - - +
341C LEU* 1.3 67.1 + - + +
343C SER* 3.0 22.2 + - - -
344C THR* 3.6 5.2 + - - -
561C ILE* 5.9 1.8 - - + -
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Residues in contact with LEU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C TRP* 3.7 19.5 - - + -
337C SER 3.1 21.7 + - - +
338C THR 3.9 1.6 - - - +
340C VAL* 1.3 76.7 - - + +
342C LEU* 1.3 63.2 + - - +
344C THR* 3.3 27.0 + - - +
347C LEU* 3.9 5.7 - - - +
479C MET* 3.4 48.2 - - + +
482C CYS* 4.4 2.9 - - + -
483C ALA* 4.2 9.0 - - + +
547C TRP* 3.8 32.1 - - + -
550C TRP* 4.1 18.1 - - + +
558C ALA* 6.1 0.4 - - + -
561C ILE* 4.4 8.5 - - + -
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C ARG* 3.4 21.4 + - - +
338C THR* 3.1 32.2 + - + +
340C VAL 3.3 0.4 - - - -
341C LEU* 1.3 77.9 - - - +
343C SER* 1.3 58.0 + - - +
344C THR 3.2 5.3 + - - +
347C LEU* 4.4 15.2 - - - +
348C GLU* 5.7 0.9 - - - -
351C PHE* 4.1 21.6 - - + -
356C ILE* 3.8 43.5 - - + +
359C ALA* 4.4 3.4 - - + -
360C ILE* 4.2 11.0 - - + -
476C LEU* 4.4 8.5 - - + -
479C MET* 3.5 27.5 - - + -
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Residues in contact with SER 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ASN* 5.4 6.1 + - - -
295C ARG* 3.1 20.9 + - - +
339C HIS* 3.2 10.9 + - - -
340C VAL* 3.0 15.7 + - - -
342C LEU* 1.3 74.8 - - - +
344C THR* 1.3 67.3 + - - +
345C PRO* 3.4 5.5 - - - +
348C GLU* 5.8 3.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il